X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;fp=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=bd58273faa3b795e5b8d4bb4c9ad8b0cacefc3b7;hb=3e943322f9d66e8718316ba8bd03669adce65149;hp=ce382c3af84267a67a7884241a3020e8beecd530;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index ce382c3..bd58273 100644
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -2,14 +2,18 @@ package jalview.schemes;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
+import jalview.util.Format;
 
 import java.awt.Color;
+import java.util.StringTokenizer;
 
 /**
  * A class that wraps either a simple colour or a graduated colour
  */
 public class FeatureColour implements FeatureColourI
 {
+  private static final String BAR = "|";
+
   final private Color colour;
 
   final private Color minColour;
@@ -49,6 +53,204 @@ public class FeatureColour implements FeatureColourI
   final private float deltaBlue;
 
   /**
+   * Parses a Jalview features file format colour descriptor
+   * [label|][mincolour|maxcolour
+   * |[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] Examples:
+   * <ul>
+   * <li>red</li>
+   * <li>a28bbb</li>
+   * <li>25,125,213</li>
+   * <li>label</li>
+   * <li>label|||0.0|0.0|above|12.5</li>
+   * <li>label|||0.0|0.0|below|12.5</li>
+   * <li>red|green|12.0|26.0|none</li>
+   * <li>a28bbb|3eb555|12.0|26.0|above|12.5</li>
+   * <li>a28bbb|3eb555|abso|12.0|26.0|below|12.5</li>
+   * </ul>
+   * 
+   * @param descriptor
+   * @return
+   * @throws IllegalArgumentException
+   *           if not parseable
+   */
+  public static FeatureColour parseJalviewFeatureColour(String descriptor)
+  {
+    StringTokenizer gcol = new StringTokenizer(descriptor, "|", true);
+    float min = Float.MIN_VALUE;
+    float max = Float.MAX_VALUE;
+    boolean labelColour = false;
+
+    String mincol = gcol.nextToken();
+    if (mincol == "|")
+    {
+      throw new IllegalArgumentException(
+              "Expected either 'label' or a colour specification in the line: "
+                      + descriptor);
+    }
+    String maxcol = null;
+    if (mincol.toLowerCase().indexOf("label") == 0)
+    {
+      labelColour = true;
+      mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+      // skip '|'
+      mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+    }
+
+    if (!labelColour && !gcol.hasMoreTokens())
+    {
+      /*
+       * only a simple colour specification - parse it
+       */
+      Color colour = UserColourScheme.getColourFromString(descriptor);
+      if (colour == null)
+      {
+        throw new IllegalArgumentException("Invalid colour descriptor: "
+                + descriptor);
+      }
+      return new FeatureColour(colour);
+    }
+
+    /*
+     * autoScaled == true: colours range over actual score range; autoScaled ==
+     * false ('abso'): colours range over min/max range
+     */
+    boolean autoScaled = false;
+    String tok = null, minval, maxval;
+    if (mincol != null)
+    {
+      // at least four more tokens
+      if (mincol.equals("|"))
+      {
+        mincol = "";
+      }
+      else
+      {
+        gcol.nextToken(); // skip next '|'
+      }
+      maxcol = gcol.nextToken();
+      if (maxcol.equals("|"))
+      {
+        maxcol = "";
+      }
+      else
+      {
+        gcol.nextToken(); // skip next '|'
+      }
+      tok = gcol.nextToken();
+      gcol.nextToken(); // skip next '|'
+      if (tok.toLowerCase().indexOf("abso") != 0)
+      {
+        minval = tok;
+        autoScaled = true;
+      }
+      else
+      {
+        minval = gcol.nextToken();
+        gcol.nextToken(); // skip next '|'
+      }
+      maxval = gcol.nextToken();
+      if (gcol.hasMoreTokens())
+      {
+        gcol.nextToken(); // skip next '|'
+      }
+      try
+      {
+        if (minval.length() > 0)
+        {
+          min = new Float(minval).floatValue();
+        }
+      } catch (Exception e)
+      {
+        throw new IllegalArgumentException(
+                "Couldn't parse the minimum value for graduated colour ("
+                        + descriptor + ")");
+      }
+      try
+      {
+        if (maxval.length() > 0)
+        {
+          max = new Float(maxval).floatValue();
+        }
+      } catch (Exception e)
+      {
+        throw new IllegalArgumentException(
+                "Couldn't parse the maximum value for graduated colour ("
+                        + descriptor + ")");
+      }
+    }
+    else
+    {
+      // add in some dummy min/max colours for the label-only
+      // colourscheme.
+      mincol = "FFFFFF";
+      maxcol = "000000";
+    }
+
+    /*
+     * construct the FeatureColour
+     */
+    FeatureColour featureColour;
+    try
+    {
+      featureColour = new FeatureColour(
+              new UserColourScheme(mincol).findColour('A'),
+              new UserColourScheme(maxcol).findColour('A'), min, max);
+      featureColour.setColourByLabel(labelColour);
+      featureColour.setAutoScaled(autoScaled);
+      // add in any additional parameters
+      String ttype = null, tval = null;
+      if (gcol.hasMoreTokens())
+      {
+        // threshold type and possibly a threshold value
+        ttype = gcol.nextToken();
+        if (ttype.toLowerCase().startsWith("below"))
+        {
+          featureColour.setBelowThreshold(true);
+        }
+        else if (ttype.toLowerCase().startsWith("above"))
+        {
+          featureColour.setAboveThreshold(true);
+        }
+        else
+        {
+          if (!ttype.toLowerCase().startsWith("no"))
+          {
+            System.err.println("Ignoring unrecognised threshold type : "
+                    + ttype);
+          }
+        }
+      }
+      if (featureColour.hasThreshold())
+      {
+        try
+        {
+          gcol.nextToken();
+          tval = gcol.nextToken();
+          featureColour.setThreshold(new Float(tval).floatValue());
+        } catch (Exception e)
+        {
+          System.err.println("Couldn't parse threshold value as a float: ("
+                  + tval + ")");
+        }
+      }
+      if (gcol.hasMoreTokens())
+      {
+        System.err
+                .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+        while (gcol.hasMoreTokens())
+        {
+          System.err.println("|" + gcol.nextToken());
+        }
+        System.err.println("\n");
+      }
+      return featureColour;
+    } catch (Exception e)
+    {
+      throw new IllegalArgumentException(e.getMessage());
+    }
+  }
+
+  /**
    * Default constructor
    */
   public FeatureColour()
@@ -63,8 +265,8 @@ public class FeatureColour implements FeatureColourI
    */
   public FeatureColour(Color c)
   {
-    minColour = null;
-    maxColour = null;
+    minColour = Color.WHITE;
+    maxColour = Color.BLACK;
     minRed = 0f;
     minGreen = 0f;
     minBlue = 0f;
@@ -418,4 +620,54 @@ public class FeatureColour implements FeatureColourI
     return isAboveThreshold() || isBelowThreshold();
   }
 
+  @Override
+  public String toJalviewFormat(String featureType)
+  {
+    String colourString = null;
+    if (isSimpleColour())
+    {
+      colourString = Format.getHexString(getColour());
+    }
+    else
+    {
+      StringBuilder sb = new StringBuilder(32);
+      if (isColourByLabel())
+      {
+        sb.append("label");
+        if (hasThreshold())
+        {
+          sb.append(BAR).append(BAR).append(BAR);
+        }
+      }
+      if (isGraduatedColour())
+      {
+        sb.append(Format.getHexString(getMinColour())).append(BAR);
+        sb.append(Format.getHexString(getMaxColour())).append(BAR);
+        if (isAutoScaled())
+        {
+          sb.append("abso").append(BAR);
+        }
+      }
+      if (hasThreshold() || isGraduatedColour())
+      {
+        sb.append(getMin()).append(BAR);
+        sb.append(getMax()).append(BAR);
+        if (isBelowThreshold())
+        {
+          sb.append("below").append(BAR).append(getThreshold());
+        }
+        else if (isAboveThreshold())
+        {
+          sb.append("above").append(BAR).append(getThreshold());
+        }
+        else
+        {
+          sb.append("none");
+        }
+      }
+      colourString = sb.toString();
+    }
+    return String.format("%s\t%s", featureType, colourString);
+  }
+
 }